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At the end of Lennon's clinical medical residency he did something different and did a short rotation at a government research lab. They did animal research, mainly rats and mice and it was the precursor to the program that eventually involved River Tam. But when Lennon was there it was just genetic neuromanipulation of rats to "weaponize" them by increasing aggression and psychic ability.

Lennon was not originally afraid of rats until he spent sometime in the research lab as a resident. Those rats there were altered to communicate telepathically with each other and so they exhibited coordinated activities; often hundreds of them all acting in unison. They were also unstable so their behavior was bizarre and violent.

Since Lennon was the resident, he was the low man on the totem pole and therefore was responsible for observing the rats at night. Rats are more active at night so Lennon saw some of their more extreme behaviors. He occasionally thought the rats were plotting against him, getting out of their cages, moving his stuff… They seemed to know he was alone, that it was dark and creepy, and so they were taking advantage of his growing squeamishness. At first Lennon thought it was in his imagination and he tried to ignore it; after all, they were just rats. But finally it became totally obvious that it wasn’t and that’s when Lennon started to worry about the rats and what the experimentation was doing to them.

Even the other researchers noticed that the rats behaved differently around Lennon and began involving him more in their experiments. They also tried to enlist him to the project after his residency ended. Lennon declined this offer, though he did finish out the assignment.

Since one of Lennon’s duties was a cage census each night, he knew that rats were escaping into the city and beyond. His opinion of rats changed after the assignment so that he jumped when he saw one and was reluctant to go into places where he might find them. It wasn’t until after the war, however, that Lennon started worrying about shipboard rats as it occurred to him that now, some of those escaped rats from Londinium might have gotten out into the black and were breeding.

Lennon didn't like the unspoken idea that someday, these techniques might be used on human beings. It is one of the many reasons he decided the Alliance was not the right side for him. He has no idea whether or not any of the experimentation he witnessed was ever tried on people; he is, however, very concerned that some of those weaponized psychic rats got out of the lab, escaped on to ships, and are now breeding. Lennon doesn't like any rodents, but he is particularly squeamish about those he might find on the core worlds, on ships that have been to core worlds, or on terraformed planets that have had contact with ships that may have come from core worlds. (pretty much all rats everywhere then.)

He makes regular sweeps through the Yellow Submarine, particularly after it has docked with core world ships or skyplexes.

He initially started with traps on the Yellow Submarine, and then pulling a few panels to make visual inspections. Lennon is a guy without a lot of hobbies and a lot of thoughts. The longer he’s been out with the Sub and its crew, the more he wants to protect them and the more the idea that such a seemingly innocuous threat might make its way onto the ship and hurt them becomes unbearable to him. Now, he has the "Almighty Rat Cannon" and will rip the ship apart to make sure there aren't any rats on board.

In other words, his fear is based on reality. The rats were real and Lennon had every reason to be afraid of them. Rats really did escape and his speculation that the escaped rats have bred with wild rats is reasonable. Whether or not these hybrid rats are getting on the ship is the only debatable aspect. Most important: his desire to protect his friends and his ship against that potential threat is very real.